Proteomic and functional annotation datasets supporting: Deep learning-assisted proteomic dissection reveals sex-specific and shared mechanisms in Populus deltoides under waterlogging stress and subsequent recovery

<p>This dataset contains the complete proteomic and functional annotation data supporting the publication <i>“Deep learning-assisted proteomic dissection reveals sex-specific and shared mechanisms in <i>Populus deltoides</i> under waterlogging stress and subsequent recovery.”</i> The data include differential expression analyses, Gene Ontology (GO) enrichment, Cluster of Orthologous Groups (COG) classification, and comparative Venn/UpSet plots for male and female <i>P. deltoides</i> under control, waterlogging, and recovery conditions.</p> <p>The dataset provides an integrative resource for exploring sex-dimorphic proteomic responses and functional pathways in <i>P. deltoides</i>. It is suitable for meta-analyses, comparative studies, and benchmarking of stress-responsive proteomes in perennial tree species.</p> <p><b>Contents:</b></p><ul><li><b>DEPs and Annotations.xlsx</b> — Complete list of quantified and differentially expressed proteins with functional annotations (accessions, fold-change, p-values, GO, KEGG terms).</li><li><b>Downregulated_proteins_Venn_UpSet.xlsx</b> — Shared and unique downregulated proteins across male and female comparisons.</li><li><b>Upregulated_proteins_Venn_UpSet.xlsx</b> — Shared and unique upregulated proteins across comparisons.</li><li><b>Gene_Ontology_terms_With_zscores.xlsx</b> — Enriched GO terms (Biological Process, Molecular Function, Cellular Component) with corresponding z-scores and FDR values.</li><li><b>MWvsFW_Go_term.xlsx</b> — GO enrichment results for male versus female plants under waterlogging stress.</li><li><b>MWRvsFWR_Go_term.xlsx</b> — GO enrichment results for male versus female plants during recovery following waterlogging.</li><li><b>MCvsFC_Go_term.xlsx</b> — Baseline GO term comparison between male and female plants under control conditions.</li><li><b>Proteins_COG_Analysis.xlsx</b> — COG functional classification of identified proteins across treatments.</li></ul> <p>All analyses were performed using R (v4.5.1) and Python (v3.12) pipelines described in the manuscript and supplementary methods. The dataset ensures transparency, reproducibility, and accessibility of proteomic and computational analyses in tree stress physiology and is fully archived in Zenodo.</p>